Required Powerpoint Slides
This is not a test, but it is to show your practical work and understanding.
Don't worry about your English. My Japanese is much worse!
If I can understand you, you get credit. Ask for help.
Your completed Powerpoint will be graded.
Discuss with other students in the class.
Ask for help often! Your TA's can help you!
You will not present your Powerpoint with the projector. It will simply be a record of your work.
Email your Powerpoint files to emartz@microbio.umass.edu.

Name your Powerpoint file with your name:
namba.ppt, minamino.pptx
Please put the slide number on each slide: "Slide 1", etc.

Slide 1

Your name.

Your email address.

Name of Professor of your laboratory research group.

Topic of your research project.

You have 2 PDB codes: One that you selected, and one that was given to you by Minamino-san
and the TA's.
If the PDB code that you selected does not have ligand, give the following information
on Slide 1 for two PDB codes: your selected code, and your given code:

Name and function of the molecule.

PDB Code.

Resolution, R value, and Free R of this model. (See #34 on the Syllabus.)

If the PDB code that you selected has ligand, use
it for all slides below.

If the PDB code that you selected has NO ligand, use
the PDB code given to you for Slides 3 and 7.
Use the PDB code that you selected for all the other slides.

Slide 2

Number of chains of protein, DNA, or RNA
in the asymmetric unit (published PDB file).
Snapshot.

How to Make a Snapshot
These instructions are for FirstGlance in Jmol, but work equally well
for molecular scenes in Proteopedia.
When you need Ångstroms, copy this into Powerpoint: Å

Slide 3 (Which PDB code? See note above.)

What are the 3-letter codes, and full names of the:

Ligands?

Non-standard residues?
Suggestions: Use Proteopedia's green links.

Slide 4

What secondary structures are present? Is the molecule mostly one
secondary structure? Snapshot.

Number of disulfide bonds within chains? Between chains?
Snapshot.
Suggestion: FirstGlance in Jmol, More Views.., Disulfide Bonds.

Snapshot of a close-up of a few noncovalent
bonds, using Contacts in FirstGlance. Zoom in. Show only a subset of all
the contacts, such as some of the putative hydrogen bonds. Show distances.
Say the kind of non-covalent bond for each one you are showing.

Show a
snapshot of the listed cation-pi interaction with a distance monitor.

Slide 14

Color your molecule by uncertainty.

List one residue with a high temperature (e.g. in the format Glu114:B).

Put halos around the atoms of the listed residue with Find.

Show a
snapshot of your molecule spacefilled, colored by temperature.
Orient the molecule to show the region with highest temperature, and the halos on the
listed residue.

Slide 15

Are there any patches of all positive or all negative charges?
Snapshot.

Choose a chain for charge calculations. Specify the one-letter name of the chain.

What is the isoelectric pH of the chain?

What is the charge of this chain at pH 4?

What is the charge of this chain at pH 7?

What is the charge of this chain at pH 10?

Slide 16

Show a publication-quality view of your molecule created with Polyview-3D.

Slide 17

Show a publication-quality rotating animation of your molecule created with Polyview-3D.
Keep the animation small (300 pixels) to avoid overloading the server. Also, rotate
through 30 degrees in 2 degree steps to minimize server load.